From 842378276ab4c4a8dabd02324bb24b8da39c4384 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 18 Oct 2019 10:28:34 +0000
Subject: [PATCH] Done and implemented compression. It doesn't segfaults at the moment
---
src/snapshot.c | 178 ++++++++++++++++++++++++++++++++++++++++------------------
1 files changed, 122 insertions(+), 56 deletions(-)
diff --git a/src/snapshot.c b/src/snapshot.c
index 6bbefdb..3a4de89 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -1,3 +1,5 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdio.h>
#include<general.h>
#include<snapshot.h>
@@ -5,7 +7,11 @@
#include<stdarg.h>
#include <zlib.h>
#include<inttypes.h>
-
+#include<config.h>
+#include <time.h>
+#include <string.h>
+#include "io.h"
+/* a helper function that utilizes ts_string data structure and performs same as sprintf */
ts_uint ts_sprintf(ts_string *str, char *fmt, ...){
va_list ap;
va_start(ap,fmt);
@@ -15,11 +21,11 @@
return n;
}
-
+/* outputs additional data into paraview xml file */
ts_bool xml_trisurf_data(FILE *fh, ts_vesicle *vesicle){
ts_string *data=(ts_string *)malloc(sizeof(ts_sprintf));
- data->string=(char *)malloc(512000*sizeof(char)); /*TODO: warning, can break if the string is to long */
+ data->string=(char *)malloc(5120000*sizeof(char)); /*TODO: warning, can break if the string is to long */
data->beg=0;
xml_trisurf_header(fh, vesicle);
@@ -27,28 +33,48 @@
xml_trisurf_tria_neigh(data,vesicle->tlist);
xml_trisurf_vtx_neigh(data,vesicle->vlist);
xml_trisurf_vtx_tristar(data,vesicle->vlist);
-#ifdef COMPRESSION
+ xml_trisurf_nucleus(data,vesicle);
+ xml_trisurf_constvolarea(data,V0,A0);
+//#ifdef COMPRESSION
char *compressed;
- ts_uint nbytes=ts_compress_string64(data->string, data->beg, &compressed);
+ ts_uint nbytes=ts_compress_string64(data->string, data->beg-1, &compressed); //suppress null character at the end with by substracting 1
fwrite(compressed, sizeof(unsigned char), nbytes, fh);
free (compressed);
-#else
- fprintf(fh,"%s", data->string);
-#endif
- free(data->string);
+//#else
+// fprintf(fh,"%s", data->string);
+//#endif
+ free(data->string); /* TODO: valgrind is not ok with this! */
free(data);
xml_trisurf_footer(fh);
return TS_SUCCESS;
}
ts_bool xml_trisurf_header(FILE *fh, ts_vesicle *vesicle){
- fprintf(fh, "<trisurfversion></trisurfversion>\n");
- fprintf(fh, "<trisurfdate></trisurfdate>\n");
- fprintf(fh, "<dumpdate></dumpdate>\n");
- fprintf(fh, "<tape>\n");
-
+/* format current time */
+ time_t current_time;
+ char *c_time_string;
+ current_time = time(NULL);
+ c_time_string = ctime(¤t_time);
+ int npoly, nfono;
+
+ fprintf(fh, "<trisurfversion>Trisurf (commit %s), compiled on %s %s</trisurfversion>\n",TS_VERSION, __DATE__, __TIME__);
+ fprintf(fh, "<dumpdate>%s</dumpdate>\n", c_time_string);
+
+ fprintf(fh, "<tape>");
+ fprintf(fh,"%s",tapetxt);
fprintf(fh, "</tape>\n");
- fprintf(fh, "<trisurf nvtx=\"%u\" npoly=\"%u\" nfono=\"%u\">\n", vesicle->vlist->n, vesicle->poly_list->n, vesicle->poly_list->poly[0]->vlist->n);
+ if(vesicle->poly_list!=NULL){
+ npoly=vesicle->poly_list->n;
+ if(npoly!=0){
+ nfono=vesicle->poly_list->poly[0]->vlist->n;
+ } else {
+ nfono=0;
+ }
+ } else {
+ npoly=0;
+ nfono=0;
+ }
+ fprintf(fh, "<trisurf nvtx=\"%u\" npoly=\"%u\" nmono=\"%u\" compressed=\"false\">\n", vesicle->vlist->n, npoly, nfono);
return TS_SUCCESS;
}
@@ -59,11 +85,11 @@
ts_bool xml_trisurf_tria(ts_string *data, ts_triangle_list *tlist){
ts_uint i;
- ts_sprintf(data,"<tria>\n");
+ ts_sprintf(data,"<tria>");
for(i=0; i<tlist->n;i++){
- ts_sprintf(data,"%u %u %u\n",tlist->tria[i]->vertex[0]->idx, tlist->tria[i]->vertex[1]->idx, tlist->tria[i]->vertex[2]->idx);
+ ts_sprintf(data,"%u %u %u ",tlist->tria[i]->vertex[0]->idx, tlist->tria[i]->vertex[1]->idx, tlist->tria[i]->vertex[2]->idx);
}
- ts_sprintf(data,"</tria>\n");
+ ts_sprintf(data,"</tria>");
return TS_SUCCESS;
}
@@ -71,7 +97,7 @@
ts_uint i;
ts_sprintf(data,"<trianeigh>\n");
for(i=0; i<tlist->n;i++){
- ts_sprintf(data,"%u %u %u\n",tlist->tria[i]->neigh[0]->idx, tlist->tria[i]->neigh[1]->idx, tlist->tria[i]->neigh[2]->idx);
+ ts_sprintf(data,"%u %u %u ",tlist->tria[i]->neigh[0]->idx, tlist->tria[i]->neigh[1]->idx, tlist->tria[i]->neigh[2]->idx);
}
ts_sprintf(data,"</trianeigh>\n");
return TS_SUCCESS;
@@ -84,7 +110,7 @@
for(j=0;j<vlist->vtx[i]->neigh_no;j++){
ts_sprintf(data,"%u ",vlist->vtx[i]->neigh[j]->idx);
}
- ts_sprintf(data, "</vtxn>\n");
+ ts_sprintf(data, "</vtxn>");
}
return TS_SUCCESS;
}
@@ -96,39 +122,87 @@
for(j=0;j<vlist->vtx[i]->tristar_no;j++){
ts_sprintf(data,"%u ",vlist->vtx[i]->tristar[j]->idx);
}
- ts_sprintf(data, "</tristar>\n");
+ ts_sprintf(data, "</tristar>");
}
return TS_SUCCESS;
}
+ts_bool xml_trisurf_nucleus(ts_string *data, ts_vesicle* vesicle){
+ if(vesicle->R_nucleus>0.0 || (vesicle->R_nucleusX>0.0 && vesicle->R_nucleusY>0.0 && vesicle->R_nucleusZ>0.0)){
+ ts_sprintf(data,"<nucleus>%.17e %.17e %.17e</nucleus>",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
+ }
+ return TS_SUCCESS;
+}
+ts_bool xml_trisurf_constvolarea(ts_string *data, ts_double volume, ts_double area){
+ ts_sprintf(data,"<constant_volume>%.17e</constant_volume>",volume);
+ ts_sprintf(data,"<constant_area>%.17e</constant_area>",area);
+ return TS_SUCCESS;
+}
/* UTILITIES */
/* zlib compression base64 encoded */
/* compressed must not be pre-malloced */
-ts_uint ts_compress_string64(char *data, ts_uint data_len, char **compressed){
+/* taken from https://gist.github.com/arq5x/5315739 */
+ts_uint ts_compress_data(char *data, ts_uint data_len, char **compressed){
z_stream defstream;
defstream.zalloc = Z_NULL;
defstream.zfree = Z_NULL;
defstream.opaque = Z_NULL;
defstream.avail_in = data_len+1;
defstream.next_in = (unsigned char *)data;
- char *compr=(char *)malloc(data_len*sizeof(char *));
+ char *compr=(char *)malloc(data_len*sizeof(char));
defstream.avail_out = data_len+1;
defstream.next_out = (unsigned char *)compr;
- deflateInit(&defstream, Z_BEST_COMPRESSION);
+ deflateInit(&defstream, 6);
+// deflateInit(&defstream, Z_BEST_COMPRESSION);
deflate(&defstream, Z_FINISH);
deflateEnd(&defstream);
- /*base64 encode*/
+ *compressed=compr;
+ return defstream.total_out;
+}
+
+ts_uint ts_compress_string64(char *data, ts_uint data_len, char **encoded_compressed){
size_t nbase;
- *compressed=base64_encode((unsigned char *)compr,(size_t)defstream.total_out,&nbase);
- //fwrite(base64, sizeof(unsigned char), nbase, fh);
+ char *compr;
+ size_t number_of_compressed_bytes=ts_compress_data(data, data_len, &compr);
+ *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase);
free(compr);
return nbase;
}
+char *ts_compress(char *data, ts_uint data_len){
+ size_t nbase1, nbase2;
+ unsigned char *compr=(unsigned char *)malloc(data_len);
+ size_t number_of_compressed_bytes=data_len;
+
+ compress(compr,&number_of_compressed_bytes, (unsigned char *)data, data_len);
+// printf("Compressdion error code=%d, Z_OK=%d, Z_BUF_ERROR=%d", errcode, Z_OK, Z_BUF_ERROR);
+
+ char *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase1);
+
+ free(compr);
+
+ ts_uint header[4]={1, data_len, data_len, number_of_compressed_bytes};
+
+ char *encoded_header=(char *)base64_encode((unsigned char *)header, 4*sizeof(ts_uint), &nbase2);
+ char *return_value=malloc((nbase1+nbase2+1)*sizeof(char));
+ strncpy(return_value,encoded_header,nbase2);
+ strncpy(return_value+nbase2,encoded_compressed,nbase1);
+ *(return_value+nbase1+nbase2)=0;
+
+// printf("Compressed size in bytes= %ld, size of encoded header= %ld, size of encoded compressed= %ld.\n",number_of_compressed_bytes, nbase2, nbase1);
+ free(encoded_compressed);
+ free(encoded_header);
+ return return_value;
+}
+
+ts_uint ts_decompress_string64(char *b64, ts_uint data_len, char **decompressed){
+return TS_SUCCESS;
+
+}
/* base64 encoding, taken from http://stackoverflow.com/questions/342409/how-do-i-base64-encode-decode-in-c */
static char encoding_table[] = {'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H',
@@ -143,10 +217,7 @@
static int mod_table[] = {0, 2, 1};
-char *base64_encode(const unsigned char *data,
- size_t input_length,
- size_t *output_length) {
-
+char *base64_encode(const unsigned char *data, size_t input_length, size_t *output_length) {
*output_length = 4 * ((input_length + 2) / 3);
int i,j;
char *encoded_data = malloc(*output_length);
@@ -154,29 +225,25 @@
for (i = 0, j = 0; i < input_length;) {
- uint32_t octet_a = i < input_length ? (unsigned char)data[i++] : 0;
- uint32_t octet_b = i < input_length ? (unsigned char)data[i++] : 0;
- uint32_t octet_c = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t octet_a = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t octet_b = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t octet_c = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t triple = (octet_a << 0x10) + (octet_b << 0x08) + octet_c;
- uint32_t triple = (octet_a << 0x10) + (octet_b << 0x08) + octet_c;
-
- encoded_data[j++] = encoding_table[(triple >> 3 * 6) & 0x3F];
- encoded_data[j++] = encoding_table[(triple >> 2 * 6) & 0x3F];
- encoded_data[j++] = encoding_table[(triple >> 1 * 6) & 0x3F];
- encoded_data[j++] = encoding_table[(triple >> 0 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 3 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 2 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 1 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 0 * 6) & 0x3F];
}
for (i = 0; i < mod_table[input_length % 3]; i++)
- encoded_data[*output_length - 1 - i] = '=';
+ encoded_data[*output_length - 1 - i] = '=';
return encoded_data;
}
-unsigned char *base64_decode(const char *data,
- size_t input_length,
- size_t *output_length) {
-
+unsigned char *base64_decode(const char *data, size_t input_length, size_t *output_length) {
int i,j;
if (decoding_table == NULL) build_decoding_table();
@@ -190,22 +257,21 @@
if (decoded_data == NULL) return NULL;
for (i = 0, j = 0; i < input_length;) {
+ uint32_t sextet_a = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
+ uint32_t sextet_b = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
+ uint32_t sextet_c = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
+ uint32_t sextet_d = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_a = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_b = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_c = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_d = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
-
- uint32_t triple = (sextet_a << 3 * 6)
+ uint32_t triple = (sextet_a << 3 * 6)
+ (sextet_b << 2 * 6)
+ (sextet_c << 1 * 6)
+ (sextet_d << 0 * 6);
- if (j < *output_length) decoded_data[j++] = (triple >> 2 * 8) & 0xFF;
- if (j < *output_length) decoded_data[j++] = (triple >> 1 * 8) & 0xFF;
- if (j < *output_length) decoded_data[j++] = (triple >> 0 * 8) & 0xFF;
+ if (j < *output_length) decoded_data[j++] = (triple >> 2 * 8) & 0xFF;
+ if (j < *output_length) decoded_data[j++] = (triple >> 1 * 8) & 0xFF;
+ if (j < *output_length) decoded_data[j++] = (triple >> 0 * 8) & 0xFF;
}
-
+ if(decoding_table !=NULL) free(decoding_table);
return decoded_data;
}
@@ -215,7 +281,7 @@
decoding_table = malloc(256);
int i;
for (i = 0; i < 64; i++)
- decoding_table[(unsigned char) encoding_table[i]] = i;
+ decoding_table[(unsigned char) encoding_table[i]] = i;
}
--
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